Supplementary Fig. 5: Live monitoring of the fusion between droplets with cells and with barcoded hydrogel beads on the microfluidic system.
From: High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer
(a) Time traces of 5 droplets showing possible fusion events occurring in all scChIP-seq experiments: droplet #1 contained a cell but no bead; droplet #2 and droplet #5 contained one bead but no cell; droplet #3 is empty; droplet #4 contained one cell plus one bead, resulting in nucleosomes barcoding. Droplets were scanned after fusion as they crossed a laser beam and their fluorescence intensity analyzed in real time. Sulforhodamine B (orange fluorescent) was used as common marker (drop-code) and Dye-405 (violet fluorescent) was used as marker of the nucleosome-containing droplets (drop-code ‘Cell’). Cells and beads were labeled with Calcein AM cellpermeant dye (green fluorescent) and Biotin-Cy5 (red fluorescent, ‘Bead-code’), respectively. (b) Scatter plot showing cell fluorescence intensity (green, ‘Cell-code’) versus bead fluorescence intensity (red, ‘Bead-code’) in each droplet allowing precise counting of the number of cells co-encapsulated with a barcoded bead. Droplets from panel (a) are indicated as examples of the different merged droplet populations. (c) Barplot showing for two scChIP-seq experiments targeting distinct histone modifications (H3K27me3 and H3K4me3), the total number of encapsulated cells detected by fluorescence on the microfluidic station, the number of cells coencapsulated with a barcoded hydrogel bead detected by fluorescence on the microfluidic station and the number of cells (that is unique barcodes) identified from the sequencing data.
